The ultimate phenome of any organism is modulated by regulated transcription of many genes. Characterization of genetic makeup is thus crucial for understanding the molecular basis of phenotypic diversity, evolution and response to intra- and extra-cellular stimuli. Living cells have evolved to perceive and integrate different signals from their surroundings and to respond by modulating the appropriate gene expression. Expressed sequence tags (ESTs) provide an invaluable resource for analysis of gene expression associated with specific organs, growth conditions, developmental processes and responses to various environmental stresses (White et al., 2000; Ewing et al., 1999; Jantasuriyarat et al., 2005). It bridges the gap between the genome sequences and gene function. ESTs have been useful for intra- and intergenomic comparisons, gene discovery, generation of single nucleotide polymorphisms (SNPs), cloning of genes from MStag peptide sequences, transcript pattern characterization, identifying splice variants, erroneous annotations in the genome database and incomplete prediction of gene structure (Ramirez et al., 2005; Udall et al., 2006). Further, the transcriptome of cells and organs comprise a focused set of transcripts that fulfills discrete but varied cellular functions. The analyses of organ specific transcriptome provide additional information about localization of gene function and pathway compartmentalization. Whereas the transcriptome research is quite advanced in animals, yeast, bacteria and reference plants like Arabidopsis and rice (Takabatake et al., 2008; Melamed et al., 2008; LeBlanc et al., 2008; Wellmer et al., 2006; Satoh et al., 2007) there is relatively less information in crop plants.
Legumes are valuable agricultural and commercial crops that serve as important nutrient sources for human diet and animal feed. About one third of human nutrition comes from legumes and in many developing countries, legumes serve as the only source of protein. Many secondary metabolites in legumes have been implicated in defense and are of particular interest as novel pharmaceuticals. Five tribes constitute the family fabaceae, of which one representative genus each from four tribes have been used to generate ESTs. However, the tribe ciceri having a single genus Cicer, remained as the understudied legume. Chickpea is the world's third most important food legume grown in over 40 countries representing all the continents. Despite its importance in plant evolution, role in human nutrition and stress adaptation, very little ESTs and differential transcriptome data is available, let alone genotype-specific gene signatures. It is grown on about 10 mha area worldwide and the global production exceeds 8 million tons. In many water-deficient regions of the world, it serves as an important protein-rich food and an increasingly valuable traded commodity. Chickpea has one of the highest nutritional compositions of edible legume and does not contain any specific major anti-nutritional factor, rather it is used in herbal medicine. Despite the importance of chickpea in the study of plant evolution, its role in nutritional requirement in humans, and stress adaptation nothing is known about the genes responsible for these traits—primarily because it is recalcitrant to genetic analysis. Unlike genetically tractable plants such as tomato, maize and Arabidopsis, chickpea produces a limited number of seeds. Furthermore, its genome is large (732 Mbp) as compared to Arabidopsis (125 Mbp). Consequently, chickpea has remained outside the realm of both modern genome-sequencing initiatives and large scale functional genomics studies. Currently available completely annotated plant genome sequences make it possible to study the genomes of agriculturally important genetically complex crop plants such as chickpea by comparing the ESTs derived from them. Only very recently, attention has been given from both genomics and proteomics perspect to this important food legume. Because of its evolutionary position as a key node within legumes as well as its nutritional and medicinal significance to humans, chickpea is ideally suited for genomic prospecting.
Transcriptional programs that regulate development and stress response are exquisitely controlled in space and time. Elucidating these programs that underlie development is essential to understand the acquisition of cell and tissue identity. Root in higher plants is a highly organized structure that plays a key role in nutrient acquisition and water uptake besides its primary function of mechanical support to the plant. Nevertheless, it is essentially the entry point for the soil borne pathogens into the plant body. Of the soil borne root pathogen, vascular wilt is the most important disease. Vascular wilt caused by Fusarium is ubiquitous evolutionarily and effects crop plants across families. In particular, chickpea wilt, is widespread in occurrence and on an average causes substantial loss of 10 to 15% in production every year worldwide. During the infection process the fungus invades roots and spreads systemically through the host's vascular system, breaking down the cell walls to form gels that block the plant's transport system thereby causing yellowing and wilting symptoms. In general, the wilt symptoms appear as chlorotic spots on the lower leaves followed by discoloration and necrosis. Vascular discoloration occurs from the roots to the young stems, followed by a yellowing and wilting of the leaves before final necrosis. When uprooted the stem is split vertically and internal discoloration is visible in pith and xylem. The susceptible genotypes take less than 25 days for wilting whereas the resistant ones do not show any symptoms of wilting up to 60 days. Fusarium, an ubiquitous pathogen that causes disease not only in plants but also is a threat to other living organisms, including human (Nucci & Anaissie, 2007; Sander et al., 1998).
Microarray technology is a powerful tool that can be used to identify the presence and level of expression of a large number of polynucleotides in a single assay. Strength of microarray technology is that it allows the identification of differential gene expression simply by comparing patterns of hybridization.
Immune responses are controlled by dynamic and variable gene expression changes which lead to reprogramming of many cellular functions. It has been postulated that the outcome of the defense response seems to be finely tuned by cross-talk between various signaling pathways (Koornneef and Pieterse, 2008) resulting in quantitative and/or kinetic effects on the resistance response (Katagiri, 2004). Basic helix-loop-helix (bHLH) transcription factors represent a family of proteins that contains a bHLH domain, a motif involved in DNA binding and dimerization (Murre et al., 1989). Members of the bHLH TF superfamily proteins are known to perform diverse regulatory functions. In animals they act as regulatory factors in different processes such as neurogenesis, cardiogenesis, myogenesis, and hematopoiesis (Jones, 2004). Although, the members of bHLH TF superfamily have been studied in mammals, but investigation of plant bHLH is still in its infancy.
The genetic improvements in plants beyond current capabilities are urgently needed for production of more food worldwide, implying thereby enhanced growth and development of plants with increased tolerance to stress. Environmental stresses including disease have major effects on agricultural production and food security. During the past, there have been attempts to develop high yielding plant varieties by engineering stress tolerance. Although there have been isolated instances of reports on developing plants with increased stress tolerance but not much has been achieved towards genetic enhancement of plants in terms of immunity. Thus, there is a critical need to discover molecules such as polynucleotides, genes, ESTs of agricultural importance, their functional analyses and exploitation for sustainable crop production.